Drug design for ever, from hype to hope (Q28732341)

3

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author name string

G Seddon

1

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V Lounnas

2

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T van den Bergh

4

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R P Bywater

5

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L Oliveira

Journal of Computer - Aided Molecular Design

6

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language of work or name

English

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publication date

January 2012

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published in

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volume

26

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issue

1

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page(s)

137-50

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cites work

A new generation of crystallographic validation tools for the protein data bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Integrating GPCR-specific information with full text articles

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Structure and function of an irreversible agonist-β(2) adrenoceptor complex

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Conserved Binding Mode of Human β 2 Adrenergic Receptor Inverse Agonists and Antagonist Revealed by X-ray Crystallography

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Calling International Rescue: knowledge lost in literature and data landslide!

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Docking ligands into flexible and solvated macromolecules. 4. Are popular scoring functions accurate for this class of proteins?

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Flexible ligand docking to multiple receptor conformations: a practical alternative

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Community benchmarks for virtual screening

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

The cost of pushing pills: a new estimate of pharmaceutical promotion expenditures in the United States

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Crystal structure of the human beta2 adrenergic G-protein-coupled receptor

17 March 2017

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

17 March 2017

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Crystal Structure of a Thermally Stable Rhodopsin Mutant

6 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Ranking poses in structure-based lead discovery and optimization: current trends in scoring function development

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

3D-QSAR study of hallucinogenic phenylalkylamines by using CoMFA approach

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Towards predictive ligand design with free-energy based computational methods?

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

How many drug targets are there?

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

The role of serendipity in drug discovery

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Scoring functions for protein-ligand docking

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

17 March 2017

PMF scoring revisited

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Investigation of substituent effect of 1-(3,3-diphenylpropyl)-piperidinyl phenylacetamides on CCR5 binding affinity using QSAR and virtual screening techniques

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Comparison of consensus scoring strategies for evaluating computational models of protein-ligand complexes

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Intrinsically unstructured proteins and their functions

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

GPCRDB information system for G protein-coupled receptors

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

The conformational plasticity of protein kinases

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Calculated conformer energies for organic molecules with multiple polar functionalities are method dependent: Taxol (case study)

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Crystal structure of rhodopsin: A G protein-coupled receptor

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

17 March 2017

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

GPCRDB: an information system for G protein-coupled receptors

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Development and validation of a genetic algorithm for flexible docking

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Automated docking of flexible ligands: applications of AutoDock

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Comparative protein modelling by satisfaction of spatial restraints

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

WHAT IF: a molecular modeling and drug design program

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

970 Million Druglike Small Molecules for Virtual Screening in the Chemical Universe Database GDB-13

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Ligand efficiency: a useful metric for lead selection

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

PDB_REDO: automated re-refinement of X-ray structure models in the PDB.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Systems-biology approaches for predicting genomic evolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

In silico identification of new ligands for GPR17: a promising therapeutic target for neurodegenerative diseases

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Incorporation of evolutionary information into Rosetta comparative modeling

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Structure-guided fragment-based in silico drug design of dengue protease inhibitors.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Prospects for the automated extraction of mutation data from the scientific literature

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Trainable structure-activity relationship model for virtual screening of CYP3A4 inhibition.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

The alpha/beta-hydrolase fold 3DM database (ABHDB) as a tool for protein engineering

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

3DM: systematic analysis of heterogeneous superfamily data to discover protein functionalities.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Docking flexible ligands in proteins with a solvent exposure- and distance-dependent dielectric function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Understanding protein non-folding.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Comparative virtual screening and novelty detection for NMDA-GlycineB antagonists

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Second-generation de novo design: a view from a medicinal chemist perspective

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

DFT-based QSAR and QSPR models of several cis-platinum complexes: solvent effect

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Re-refinement from deposited X-ray data can deliver improved models for most PDB entries

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

What induces pocket openings on protein surface patches involved in protein-protein interactions?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Docking and scoring with alternative side-chain conformations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

A ligand's-eye view of protein binding.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Conformational thermostabilization of the beta1-adrenergic receptor in a detergent-resistant form

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Protein-ligand docking with multiple flexible side chains

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

QSAR analyses on avian influenza virus neuraminidase inhibitors using CoMFA, CoMSIA, and HQSAR.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Development and application of hybrid structure based method for efficient screening of ligands binding to G-protein coupled receptors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Inactive and active states and supramolecular organization of GPCRs: insights from computational modeling

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

A combined ligand-based and target-based drug design approach for G-protein coupled receptors: application to salvinorin A, a selective kappa opioid receptor agonist.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Protein Alpha Shape (PAS) Dock: a new gaussian-based score function suitable for docking in homology modelled protein structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Scoring functions--the first 100 years.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Validation of an empirical RNA-ligand scoring function for fast flexible docking using Ribodock

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Heavier-than-air flying machines are impossible.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Comparative study of several algorithms for flexible ligand docking

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Modeling of enzyme-substrate complexes for the metalloproteases MMP-3, ADAM-9 and ADAM-10.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Comparison of support vector machine and artificial neural network systems for drug/nondrug classification

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

FDS: flexible ligand and receptor docking with a continuum solvent model and soft-core energy function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Implications of protein flexibility for drug discovery

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Treatment of antidepressant-associated sexual dysfunction with sildenafil: a randomized controlled trial

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Further development and validation of empirical scoring functions for structure-based binding affinity prediction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Prediction of 'drug-likeness'.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Binding mode prediction for a flexible ligand in a flexible pocket using multi-conformation simulated annealing pseudo crystallographic refinement

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Mutational analysis of the antagonist-binding site of the histamine H(1) receptor

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

DREAM++: flexible docking program for virtual combinatorial libraries

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Comparison of two implementations of the incremental construction algorithm in flexible docking of thrombin inhibitors.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Combinatorial docking and combinatorial chemistry: design of potent non-peptide thrombin inhibitors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Evaluation of a method for controlling molecular scaffold diversity in de novo ligand design

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Data modelling with neural networks: advantages and limitations.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Genetic algorithms in molecular recognition and design

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

GroupBuild: a fragment-based method for de novo drug design

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

GenStar: a method for de novo drug design.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

A common step for signal transduction in G protein-coupled receptors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

FLOG: a system to select 'quasi-flexible' ligands complementary to a receptor of known three-dimensional structure

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

A fast and efficient method to generate biologically relevant conformations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Flexibases: a way to enhance the use of molecular docking methods

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

PRO-LIGAND: an approach to de novo molecular design. 1. Application to the design of organic molecules

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

A shape-based machine learning tool for drug design

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

PRO-LIGAND: an approach to de novo molecular design. 3. A genetic algorithm for structure refinement.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Flexible ligand docking using a genetic algorithm.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

A geometric approach to macromolecule-ligand interactions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. II. Environment of bound NADPH and implications for catalysis.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

How many medicines are there?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

A computational procedure for determining energetically favorable binding sites on biologically important macromolecules

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Future in biomolecular computation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Conformation-activity relationships of opiate analgesics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

A unique geometry of the active site of angiotensin-converting enzyme consistent with structure-activity studies

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

MOPAC: a semiempirical molecular orbital program

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Determination of the relative binding free energies of peptide inhibitors to the HIV-1 protease

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

The computer program LUDI: a new method for the de novo design of enzyme inhibitors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Conformational studies on (+)-anatoxin-a and derivatives

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

PLS modelling of structure-activity relationships of catechol O-methyltransferase inhibitors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Comparative molecular field analysis of CCK-A antagonists using field-fit as an alignment technique. A convenient guide to design new CCK-A ligands

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Conformational studies on the four stereoisomers of the novel anticholinergic 4-(dimethylamino)-2-phenyl-2-(2-pyridyl)pentanamide

20 June 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Molden: a pre- and post-processing program for molecular and electronic structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Solvent effect on the synthesis of clarithromycin: a molecular dynamics study

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Protonation-induced stereoisomerism in nicotine: conformational studies using classical (AMBER) and ab initio (Car-Parrinello) molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Dynamical aspects of TEM-1 beta-lactamase probed by molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Molecular dynamics simulation study of PTP1B with allosteric inhibitor and its application in receptor based pharmacophore modeling

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Conformational analysis. 130. MM2. A hydrocarbon force field utilizing V1 and V2 torsional terms

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Can we separate active from inactive conformations?

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Evaluating docked complexes with the HINT exponential function and empirical atomic hydrophobicities.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

A new method for estimating the importance of hydrogen-bonding groups in the binding site of a protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

An improved scoring function for suboptimal polar ligand complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Flexible docking under pharmacophore type constraints

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE).

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

An improved adaptive genetic algorithm for protein-ligand docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Ligand solvation in molecular docking.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

A fast flexible docking method using an incremental construction algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Experimental design based 3-D QSAR analysis of steroid-protein interactions: application to human CBG complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

CoMFA validation of the superposition of six classes of compounds which block GABA receptors non-competitively.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Three-dimensional quantitative structure-activity relationship (3D QSAR) and pharmacophore elucidation of tetrahydropyran derivatives as serotonin and norepinephrine transporter inhibitors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Homology modeling, force field design, and free energy simulation studies to optimize the activities of histone deacetylase inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Homology modeling and molecular interaction field studies of alpha-glucosidases as a guide to structure-based design of novel proposed anti-HIV inhibitors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Understanding and modulating cyclin-dependent kinase inhibitor specificity: molecular modeling and biochemical evaluation of pyrazolopyrimidinones as CDK2/cyclin A and CDK4/cyclin D1 inhibitors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Ligand-guided optimization of CXCR4 homology models for virtual screening using a multiple chemotype approach.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Progress of 1D protein structure prediction at last

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Molecular modelling studies on the ORL1-receptor and ORL1-agonists

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

The de novo design of median molecules within a property range of interest

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Placement of medium-sized molecular fragments into active sites of proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

BUILDER v.2: improving the chemistry of a de novo design strategy

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Automated molecular design: a new fragment-joining algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Identification of cylin-dependent kinase 1 inhibitors of a new chemical type by structure-based design and database searching

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

A successful virtual screening application: prediction of anticonvulsant activity in MES test of widely used pharmaceutical and food preservatives methylparaben and propylparaben

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Ligand efficiency indices as guideposts for drug discovery.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Compass: predicting biological activities from molecular surface properties. Performance comparisons on a steroid benchmark

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Machine learning study for the prediction of transdermal peptide.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Molecular docking studies on tetrahydroimidazo-[4,5,1-jk][1,4]-benzodiazepinone (TIBO) derivatives as HIV-1 NNRT inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Quantitative structure-activity relationships by neural networks and inductive logic programming. II. The inhibition of dihydrofolate reductase by triazines.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Identification of fungal oxaloacetate hydrolyase within the isocitrate lyase/PEP mutase enzyme superfamily using a sequence marker-based method

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Increasing the thermostability of sucrose phosphorylase by a combination of sequence- and structure-based mutagenesis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Structural biology: Breaking the protein rules

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

In Silico Veritas: The Pitfalls and Challenges of Predicting GPCR-Ligand Interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

The search for a new model structure of beta-factor XIIa

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

PDB Improvement Starts with Data Deposition

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

SCF-MO study of the polyglycine II structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

Lessons from 60 years of pharmaceutical innovation

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Computational study on the molecular inclusion of andrographolide by cyclodextrin.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

ENPDA: an evolutionary structure-based de novo peptide design algorithm.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

BRAGI: linking and visualization of database information in a 3D viewer and modeling tool

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Conformational energy penalties of protein-bound ligands

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3268973

Generation of a homology model of the human histamine H3 receptor for ligand docking and pharmacophore-based screening

27 November 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9519-9

21 January 2018

1 reference

12 December 2020

Can free energy calculations be fast and accurate at the same time? Binding of low-affinity, non-peptide inhibitors to the SH2 domain of the src protein

1 reference

12 December 2020

Ligand binding affinity prediction by linear interaction energy methods

1 reference

12 December 2020

Comparative molecular field analysis and energy interaction studies of thrombin-inhibitor complexes

1 reference

12 December 2020

Comparison of a homology model and the crystallographic structure of human 11beta-hydroxysteroid dehydrogenase type 1 (11betaHSD1) in a structure-based identification of inhibitors

1 reference

12 December 2020

PLIM: a protein-ligand interaction modeller

1 reference

12 December 2020

Development of small molecules designed to modulate protein-protein interactions

1 reference

12 December 2020

Novel tools for extraction and validation of disease-related mutations applied to Fabry disease

1 reference

12 December 2020

Study of the interaction between aryloxypropanolamines and Asn386 in helix VII of the human 5-hydroxytryptamine1A receptor

1 reference

12 December 2020

QSAR of conformationally flexible molecules: comparative molecular field analysis of protein-tyrosine kinase inhibitors

1 reference

12 December 2020

Steroid binding by antibodies and artificial receptors: exploration of theoretical methods to determine the origins of binding affinities and specificities

1 reference

12 December 2020

Homology modeling, docking and structure-based pharmacophore of inhibitors of DNA methyltransferase

1 reference

12 December 2020

Lessons from 54 years of pharmaceutical research

1 reference

12 December 2020

A new procedure for improving the predictiveness of CoMFA models and its application to a set of dihydrofolate reductase inhibitors

1 reference

12 December 2020

A CoMFA analysis with conformational propensity: an attempt to analyze the SAR of a set of molecules with different conformational flexibility using a 3D-QSAR method

1 reference

12 December 2020

Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry

1 reference

12 December 2020

The atom assignment problem in automated de novo drug design. 1. Transferability of molecular fragment properties

1 reference

12 December 2020

Symposium overview. Minnesota Conference on Supercomputing in Biology: Proteins, Nucleic Acids, and Water

1 reference

12 December 2020

A low resolution model for the interaction of G proteins with G protein-coupled receptors

1 reference

12 December 2020

Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities

1 reference

12 December 2020

HTS Technologies--IBC Informa Conference

1 reference

12 December 2020

Enhancing the accuracy of virtual screening: molecular dynamics with quantum-refined force fields

1 reference

12 December 2020

Do active site conformations of small ligands correspond to low free-energy solution structures?

1 reference

12 December 2020

On the molecular interaction between lactoferrin and the dye Red HE-3b. A novel approach for docking a charged and highly flexible molecule to protein surfaces

1 reference

12 December 2020

Docking and quantitative structure-activity relationship studies for 3-fluoro-4-(pyrrolo[2,1-f][1,2,4]triazin-4-yloxy)aniline, 3-fluoro-4-(1H-pyrrolo[2,3-b]pyridin-4-yloxy)aniline, and 4-(4-amino-2-fluorophenoxy)-2-pyridinylamine derivatives as c-Me

1 reference

12 December 2020

QSAR and conformational analysis of the antiinflammatory agent amfenac and analogues

1 reference

12 December 2020

A novel scoring function for molecular docking

1 reference

12 December 2020

PK/PD modelling and beyond: impact on drug development

1 reference

12 December 2020

An approach to computer-aided inhibitor design: application to cathepsin L

1 reference

12 December 2020

Comparison of conformer distributions in the crystalline state with conformational energies calculated by ab initio techniques

1 reference

12 December 2020

10.1007/S10822-011-9519-9

Identifiers

DOI

0 references

DBLP publication ID

journals/jcamd/SeddonLMBBOV12

1 reference

DBLP Dataset 2021-01-02